If you order an oligo to be synthesized with an amino group on one end, then our CF® Dye succinimidyl ester (SE) dyes could be used to label it using a standard amine labeling protocol for DNA.
We recommend using an HPLC purified oligo, with an amino group with a C6 linker at the 5′ or 3′ end. To remove free dye after labeling, you could use G25 Sephadex, gel purification, ethanol precipitation, or HPLC, depending on the degree of purity needed.
Alternatively, this may be something that an oligo synthesis company may be able to perform for you as a custom labeling.
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